This module can be used to create position-weight matrices (PWM)
to describe a DNA motif. Such matrices can then be searched on
a DNA sequence, given a threshold for alignment score.

module Biocaml_pwm:

sig

typecount_matrix = int array array

Type to represent gap-free alignments. First dimension is
the sequence position, second dimension is for the alphabet.
Only DNA alphabet (A, C, G, T) is supported to rows should be
of length exactly four.

tandem orientation spacer cm1 cm2 bg builds a PWM by constructing
a composite motif: it builds mat1 the PWM from cm1 under background bg
(resp. mat2 from cm2 under bg), then concatenates mat1 and mat2 with
spacer non scoring columns in between